Jim Harbaugh-led San Francisco 49ers don't just play better, they scheme better

San Francisco 49ers head coach Jim Harbaugh applauds to his players after they scored a touchdown against the San Diego Chargers in the first half of a preseason game at Candlestick Park, in San Francisco, Calif., on Thursday, Aug. 30, 2012. (Ray Chavez/Staff)

SANTA CLARA -- There was a time not long ago when everyone in the stadium -- opposing defenses included -- could reasonably assume that a 49ers' first-down play would be a handoff to Frank Gore.

But with Jim Harbaugh and his pair of savvy coordinators at the helm, the 49ers aren't just outplaying teams during their 3-1 start. They're also outsmarting them. The head coach who keeps a photo of Bill Walsh taped to his office computer has restored the art of the chess match on both sides of the ball.

Far from the smash-mouth simplicity of previous regimes, the 49ers are tormenting opponents with frequent personnel substitutions, complex schemes and an offense that features more wrinkles than a retirement home.

Consider the game film the Buffalo Bills (2-2) must study in advance of Sunday's game at Candlestick Park. The tape will show that against the New York Jets last week the 49ers unleashed backup quarterback Colin Kaepernick as a runner, passer and receiver.

The 49ers ran not one but two quarterback read options, gave the ball to Mario Manningham on and end around and faked the ball on an end around to Ted Ginn Jr.

And that was just in the first half. What new tricks will the 49ers have in store this week?

"I don't look at them as trick plays -- they're football plays," offensive coordinator Greg Roman explained Thursday. "I call 'em 'mixers.' You mix 'em in from time to time."

In the least, the 49ers are mixing up their opponents.

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"They have different wide receivers in almost every package. It's hard to get a bead on any one thing," Detroit Lions coach Jim Schwartz in the days leading up to a Week 2 visit to Candlestick Park. "A lot of shifts, a lot of motions. It definitely spreads your attention to different places, which I think is what it's all designed to do."

Take the 49ers' opening drive against the Lions: As the play clock ticked down on a first-and-10 from the Detroit 21, a national television audience heard Alex Smith barking, "Kill! Kill! Kill!" The quarterback was changing the play at the line of scrimmage.

With just 5 seconds to go on the play clock, Smith gestured for fullback Bruce Miller to go into motion. When Miller raced to line up as a receiver split wide left, a Lions linebacker followed.

Just like that, the 49ers orchestrated a ridiculous mismatch: Pro Bowl tight end Vernon Davis was isolated against John Wendling, a backup safety who was the field only because Louis Delmas was injured.

Leaving the Lions no time to adjust, Smith snapped the ball with a nanosecond to spare. Davis roared past Wendling and caught the ball in the end zone to complete a breezy four-play drive. Taking up just 1 minute, 12 seconds, it was the 49ers' fastest opening-drive touchdown in eight years.

"That isn't something the 49ers could have done in Week 2 a year ago," NBC broadcaster Cris Collinsworth marveled after the play unfolded.

Indeed, a year ago, the prolonged NFL lockout prevented Harbaugh and his staff from introducing all of the complexities from his offensive playbook, a system he recently acknowledged can take a few years to learn.

The schemes require constantly changing personnel -- and the more unpredictable the better, such as sending 6-foot-6, 355-pound offensive lineman Leonard Davis trotting onto the field as a tight end.

Roman, who followed Harbaugh from Stanford, said it dawned on them while at The Farm how much varying personnel packages could frustrate defenses.

"When you're coaching in college, you have more players at your disposal on game day. So, if guys earn the right to play and have a role during the game, you can get them out there," Roman said.

"It definitely creates a lot more for the defense to prepare for, not only in what you might do out of that personnel group, but the individual skill set of each guy. We really took that to probably a new level there (at Stanford)."

On defense, players hailed coordinator Vic Fangio's schemes after the 49ers held two of the league's most prolific passers, Aaron Rodgers of the Green Bay Packers and Matthew Stafford of the Lions, in check over the first two weeks. Those quarterbacks combined for a pedestrian 87.2 passer rating with three touchdown passes and two interceptions.

"The game plans were pretty spot on for what we thought they were going to give us," defensive end Justin Smith said.

Then, after a lousy game against the Minnesota Vikings in Week 3, the 49ers defense demolished New York 34-0 last Sunday while limiting the Jets to 145 yards. Cornerback Carlos Rogers said the 49ers knew what the Jets were going to try because Fangio had essentially cracked their code.

In general, the 49ers' defensive game plans aren't overly exotic or gimmicky. They bring extra pressure sparingly, using the element of surprise to their advantage, such as when Rogers came on a rare cornerback blitz against Rodgers in Week 1.

"You have to scheme it up, and I don't think (the Packers) were ready for the first blitz that we came with," said Rogers, who got a sack on the play. "I've played for some good coordinators, and I think (Fangio) is one of the best, if not the best. We're utilizing all of our talents on defense.

"We're recognizing the weakness of the offense. We're confusing them with our disguises."